Microbial Network Analysis Research Articles

Characteristics of airway microbiome co-occurrence network in patients with type 2 and non-type 2 asthma

Objective: To study the characteristics of the airway microbiome co-occurrence network in patients with type 2 and non-type 2 asthma. Methods: In a prospective study based on a cohort of asthma patients, respiratory induced sputum samples were collected from 55 asthma patients [25 males and 30 females, with a median age of 47.7 years (age range 34.3-63.0 years)] admitted to the Department of Respiratory and Critical Care, Beijing Chaoyang Hospital, Capital Medical University and 12 healthy controls from the Physical Examination Centre of Beijing Chaoyang Hospital, Capital Medical University, from May 2021 to May 2022. According to the level of exhaled breath nitric oxide (FeNO), the asthma patients were divided into 22 cases in the high FeNO group (FeNO≥40 ppb, i.e., type 2 asthma group) and 33 cases in the low FeNO group (FeNO<40 ppb, i.e., non-type 2 asthma group). All induced sputum samples were subjected to second-generation macrogenomic sequencing and bioinformatic analyses of microbial community diversity, compositional characteristics, symbiotic network characteristics and metabolic function prediction. The Kruskal-Wallis rank sum test was used for between-group comparisons, and the linear discriminant analysis (LEfSe) method was used to compare the differences in flora composition between groups. The R language was used for microbial network analysis. In addition, PICRUSt was used to predict the metabolic-functional characteristics of the microbial communities. Results: The microbial communities in the healthy control group had a lower proportion of p_Firmicutes and p_Proteobacteria than asthma patients, 29% and 21%, respectively; 37% and 33% in the low FeNO group and 42% and 26% in the high FeNO group. The microbial network in the low FeNO group had 64 pairs of edges forming 16 communities, and about 75% of the nodes had eigenvector centrality values between 0 and 0.05, and 25% of the nodes had eigenvector centrality values between 0.10 and 0.45. There were four layers of κ-nucleosynthesis, and about 42% of the vertices were in the centre of the two layers. The microbial network of the high-FeNO group had 80 pairs of edges forming 18 clusters, and 81% of the nodes had eigenvector centrality values between 0 and 0.05, and 19% of the nodes had eigenvector centrality values between 0.10 and 0.35. The κ-nucleus decomposition had eight layers, and 21% of the vertices were located in the centre's two layers. The main functional differences between the low and high FeNO groups were shown in metabolic pathways (including sugar, lipid, amino acid, and energy metabolism), drug resistance, biofilm transport, signalling, intercellular communication, and cellular repair. Conclusions: Compared with non-type 2 asthmatics, type 2 asthmatics had a higher alpha diversity of respiratory microbiota, lower levels of microorganisms in the p_Proteobacteria, and a more aggregated microbial network. There was a significant difference in the predicted metabolic function of the two endotypes of asthmatics.

Insight into the mechanism of alkyl polyglucose biosurfactants enhancing antibiotics resistance genes removal during biotransformation of waste activated sludge into medium-chain fatty acids

Enhancing the biodegradability of waste activated sludge (WAS) based on environmentally friendly biosurfactants alkyl polyglucose (APG) to promote the recovery of medium-chain fatty acids (MCFAs) is a promising strategy. However, the effect and underlying mechanism of APG on antibiotic resistance genes (ARGs) removal during MCFAs production by WAS anaerobic fermentation are still unclear. This study found that APG significantly enhanced the removal of ARGs during the anaerobic fermentation to produce MCFAs, and the maximum removal efficiency of total ARGs was 95.64 % in 0.3 g APG/g TSS group, which was 46.31 % higher than the control group. The increase in extracellular lactate dehydrogenase, 16S rDNA and ARGs indicated that APG strengthened the lysis of ARGs hosts, thus suppressing the vertical transfer of ARGs caused by host proliferation. Furthermore, APG facilitated the decline in the abundance of mobile gene elements and two-component system genes, which was beneficial to reduce the horizontal transfer of ARGs. Microbial community and network analysis revealed that APG enriched functional microorganism and reduced potential ARGs hosts. Finally, partial least-squares path model analysis further demonstrated that the effectiveness of APG in ARGs removal was related to the restriction of ARGs transfer and change of bacterial community.

Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort.

Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.

Activation of microbial community and enhancement of quality by inoculating Zygosaccharomyces rouxii during the post-fermentation stage of Doubanjiang

The prolonged post-fermentation stage of Doubanjiang imparts unique flavors but may reduce microbial vitality and increase contamination, affecting quality. This study investigated the effect of Zygosaccharomyces rouxii inoculation during post-fermentation. Results showed a 46.7% increase in amino nitrogen and a significant rise in volatile compounds like phenethyl alcohol, 3-methyl-1-butanol, and ethyl octanoate. The relative abundances of Staphylococcus and Pantoea increased among bacteria, while Pichia, Wickerhamiella, and Zygosaccharomyces increased among fungi. Redundancy analysis showed a positive correlation between these genera and the main volatiles. Microbial ecological network analysis showed that inoculating Z. rouxii increased nodes and edges, resulting in tighter inter-module connections and enhanced robustness. Key genera included Zygosaccharomyces, Staphylococcus, Kazachstania, and Weissella. Metaproteomic results demonstrated that upregulated proteins were predominantly enriched in pathways related to flavor formation, while downregulated proteins were associated with ribosome and DNA synthesis-related pathways. PICRUSt2 analysis results showed higher expression of enzymes related to volatiles in innoculated samples. Inoculating Z. rouxii during the post-fermentation could boost core microorganisms, curb foodborne pathogens, stabilize the microbial community, and enhance Doubanjiang quality.

Soil bacterial community characteristics and influencing factors in different types of farmland shelterbelts in the Alaer reclamation area.

To investigate the effects of various types of farmland shelterbelts on soil quality and soil bacterial community diversity, this study focused on soil samples from four different shelterbelt types in the Alaer reclamation area, including Populus euphratica Oliv.- Populus tomentosa Carrière (PP), Elaeagnus angustifolia L.- Populus euphratica Oliv. (EP), Populus alba var. pyramidalis Bunge (P), and Salix babylonica L. (S). We analyzed their physical, chemical, biological properties as well as the differences in bacterial community structure, and explored the influencing factors on soil microbial community characteristics through microbial correlation network analysis. The results showed that: (1) There were significant differences in soil properties among the four types of farmland shelterbelts (p < 0.05), with P soils exhibiting the highest levels of organic matter, total nitrogen, and total phosphorus contents. (2) The Alpha diversity indices of soil bacteria showed significant differences among the four types of farmland shelterbelts (p < 0.05), with the P soils displayed the highest Chao1 and Shannon indices. (3) There were differences in the composition and abundance of dominant soil bacterial communities among different farmland shelterbelts, notably, the abundances of Verrucomicrobia, Acidobacteria, and Planctomycetes were significantly higher in P soils compared to the other three types. (4) The complexity of the correlation network between microbial species and environmental factors was highest in EP soils, soil microbial biomass nitrogen and available phosphorus were the main influencing factors. These findings indicated that different types of farmland shelterbelts had significant impacts on soil properties and soil bacterial communities. Soil bacterial communities were regulated by soil properties, their changes reflected a combined effect of soil characteristics and tree species.

Microbial community composition and co-occurrence network analysis of the rhizosphere soil of the main constructive tree species in Helan Mountain of Northwest China

To understand the microbial diversity and community composition within the main constructive tree species, Picea crassifolia, Betula platyphylla, and Pinus tabuliformis, in Helan Mountain and their response to changes in soil physicochemical factors, a high throughput sequencing technology was used to analyze the bacterial and fungal diversity and community structure. RDA (Redundancy Analysis) and Pearson correlation analysis were used to explore the influence of soil physicochemical factors on microbial community construction, and co-occurrence network analysis was conducted on the microbial communities. The results showed that the fungal and bacterial diversity was highest in B. platyphylla, and lowest in P. crassifolia. Additionally, the fungal/bacterial richness was greatest in the rhizosphere soils of P. tabuliformis and B. platyphylla. RDA and Pearson correlation analysis revealed that NN (nitrate nitrogen) and AP (available phosphorus) were the main determining factors of the bacterial community, while NN and SOC (soil water content) were the main determining factors of the fungal community. Pearson correlation analysis between soil physicochemical factors and the alpha diversity of the microbial communities revealed a significant positive correlation between pH and the bacterial and fungal diversity, while SOC, TN (total nitrogen), AP, and AN (available nitrogen) were significantly negatively correlated with the bacterial and fungal diversity. Co-occurrence network analysis revealed that the soil bacterial communities exhibit richer network nodes, edges, greater diversity, and greater network connectivity. Indicating that bacterial communities exhibit more complex and stable interaction patterns in soil. This study reveals the complex interactive relationship between microbial communities and soil physicochemical factors in forest ecosystems. By analyzing the response of rhizosphere microbial communities of major tree species in Helan Mountain to nutrient dynamics and pH changes, we can deepen our understanding of the role of microorganisms in regulating ecosystem functions and provide theoretical basis for soil improvement and ecological restoration strategies.

Effects of artemisinin sustained-release algaecides on in-situ cyanobacterial inhibition and microbes-floating plants dominated ecosystem functions in artificial landscape lake

The artemisinin sustained-release algaecides (ASAs) have been proven to be a safe and effective mean of inhibiting cyanobacteria in laboratory experiments. However, their effectiveness and impacts on ecosystem functions (EF) in natural waters are still unclear. In this study, the in-situ inhibitory effect of ASAs on cyanobacteria in natural waters was investigated over a period of 110 days to assess EF impacts dominated by microbes and floating plants. The results indicated that ASAs had a long-term inhibitory effect on cyanobacteria. ASAs did not affect sediment but increased TOC and TP in the water column in 2–10 days. Microbial diversity and network analyses indicated that ASAs enhanced bacterial diversity, network complexity, and hub-bacteria in networks. Metabolic pathway predictions and CCA analysis showed that ASAs maintained the stability of EF by enhancing the metabolic capacities of bacteria, and the relationships between metabolic microorganisms and environmental factors. PLS-PM revealed that ASAs primarily drove bacterial resistance to cyanobacteria, which was the key mechanism for its long-term inhibition of cyanobacteria. However, the early outbreak of floating plants was not conducive to the long-term inhibition of cyanobacteria by ASAs. This study provides new insights into the mechanisms and ecological impacts of cyanobacterial inhibition by ASAs in complex aquatic environments.

Important role of Chloroflexi: Improved the cooperation of anammox community under PFOS stress

Perfluorooctane sulfonic acid (PFOS) has received extensive attention in recent years due to its persistence and biotoxicity. As an advanced biological nitrogen removal process, anaerobic ammonium oxidation (anammox) is considered to be the most promising process to replace traditional nitrogen removal technology in the future. However, it is still unclear how PFOS affects microbial community and network structure in anammox system. The study found that PFOS had little influence on the nitrogen removal efficiency. Through microbial community and network analysis, the results showed that the typical anammox bacteria (Candidatus_Kuenenia, Candidatus_Jettenia, and Candidatus_Brocadia) enriched with the increasing concentrations of PFOS. Overall network complexity and proportion of positive links was significantly increased under 10 mg/L PFOS. Especially the subnetwork of Chloroflexi owned 100 % positive links under 10 mg/L PFOS, which accounted for 53.62 % of the corresponding overall network. The genus OLB13 and norank_f__Anaerolineaceae from Chloroflexi could cooperate with anammox bacteria to resist the impact of PFOS and further maintained the stability of anammox system. This study provided new insights into the effects of perfluoroalkyl compounds on anammox system.

INAP 2.0: Harnessing metabolic complementarity in microbial network analysis.

With the widespread adoption of metagenomic sequencing, new perspectives have emerged for studying microbial ecological networks, yielding metabolic evidence of interspecies interactions that traditional co-occurrence networks cannot infer. This protocol introduces the integrated Network Analysis Pipeline 2.0 (iNAP 2.0), which features an innovative metabolic complementarity network for microbial studies from metagenomics sequencing data. iNAP 2.0 sets up a four-module process for metabolic interaction analysis, namely: (I) Prepare genome-scale metabolic models; (II) Infer pairwise interactions of genome-scale metabolic models; (III) Construct metabolic interaction networks; and (IV) Analyze metabolic interaction networks. Starting from metagenome-assembled or complete genomes, iNAP 2.0 offers a variety of methods to quantify the potential and trends of metabolic complementarity between models, including the PhyloMint pipeline based on phylogenetic distance-adjusted metabolic complementarity, the SMETANA (species metabolic interaction analysis) approach based on cross-feeding substrate exchange prediction, and metabolic distance calculation based on parsimonious flux balance analysis (pFBA). Notably, iNAP 2.0 integrates the random matrix theory (RMT) approach to find the suitable threshold for metabolic interaction network construction. Finally, the metabolic interaction networks can proceed to analysis using topological feature analysis such as hub node determination. In addition, a key feature of iNAP 2.0 is the identification of potentially transferable metabolites between species, presented as intermediate nodes that connect microbial nodes in the metabolic complementarity network. To illustrate these new features, we use a set of metagenome-assembled genomes as an example to comprehensively document the usage of the tools. iNAP 2.0 is available at https://inap.denglab.org.cn for all users to register and use for free.

Mucosal microbiota characterization in gastric cancer identifies immune-activated-related transcripts relevant gastric microbiome signatures.

Tumor microenvironment (TME) immune cells and gastric mucosal microbiome constitute two vital elements of tumor tissue. Increasing evidence has elucidated their clinicopathological significance in predicting outcomes and therapeutic efficacy. However, comprehensive characterization of immune cell-associated microbiome signatures in the TME is still in the early stages of development. Here, we characterized the gastric mucosa microbiome and its associations with immune-activated related transcripts (IATs) in 170 GC tumor tissues and matched non-tumor tissues using 16s rRNA gene sequencing and quantitative reverse transcription-PCR. Microbial diversity and richness were significantly higher in GC tumor tissues than in non-tumor tissues. Differences in microbial composition between the groups were evident, with Firmicutes, Proteobacteria, Bacteroidota, Campilobacterota, Actinobacteria, Fusobacteriota, Verrucomicrobiota, Acidobacteriota, and Cyanobacteria being the dominant phyla in the gastric mucosal microbiota. Microbial interaction network analysis revealed distinctive centralities of oral bacteria (such as Fusobacterium, Porphyromonas, Prevotella, etc.) in both tumor and normal mucosae networks, suggesting their significant influence on GC microbial ecology. Furthermore, we analyzed the expression of IATs (CXCL9, CXCL10, GZMA, GZMB, PRF1, CD8A, IFNG, TBX2, and TNF) and characterized IAT-relevant gastric microbiome signatures in GC patients. Our results showed that the expression of CXCL9, CXCL10, GZMA, GZMB, PRF1 and IFNG was significantly higher in tumor tissues than in adjacent normal tissues in GC patients. Notably, high expression of IATs in tumor tissues was associated with improved survival in GC patients and could serve as a powerful predictor for disease-free survival. Additionally, analysis of IAT levels and mucosal microbiota diversity revealed a correlation between higher IAT expression and increased microbiota richness and evenness in the IATs high group, suggesting potential interactions between mucosal microbiota and tumor immunopathology. Spearman correlation analysis showed positive associations between IAT expression and specific mucosal bacterial species. Notably, Akkermansia muciniphila demonstrated potential involvement in modulating GZMB expression in the GC mucosal microenvironment. These findings underscore the importance of mucosal microbiota alterations in GC and suggest potential therapeutic targets focusing on modulating the tumor microbiota for improved clinical outcomes. The detailed characterization of these elements has profound implications for both treatment and survival prediction in GC. We observed that microbial diversity and richness were significantly higher in GC tumor tissues compared to non-tumor tissues. These differences highlight the unique microbial landscape of GC tumors and suggest that the microbiome could influence tumor development and progression. Importantly, our study demonstrated that high expression levels of IATs in GC tumor tissues were associated with improved patient survival. This suggests that IATs not only reflect immune activation but also serve as valuable biomarkers for predicting disease-free survival. The potential of IATs as predictive markers underscores their utility in guiding therapeutic strategies and personalizing treatment approaches. Moreover, the correlation between higher IAT expression and increased microbiota richness and evenness suggests that a diverse and balanced microbiome may enhance immune responses and contribute to better clinical outcomes. These findings highlight the critical need to consider mucosal microbiota alterations in GC management. Targeting the tumor microbiota could emerge as a promising therapeutic strategy, potentially leading to more effective treatments and improved patient outcomes. Understanding and modulating the microbiome's role in GC opens new avenues for innovative therapeutic interventions and personalized medicine.

Enhanced humification attributed by the integration of Fenton reagent and oxalic acid during a co-composting of swine manure and corn straw: Impacts and the possible mechanisms

To illustrate the role and mechanism of using oxalic acid (OA) and Fenton reagent to enhance carbon transformation and humification in the co-composting of swine manure and corn straw, four different treatments, SW1 (Control), SW2 (Fenton reagent), SW3 (10 % OA), and SW4 (Fenton reagent + 10 % OA) were set up for an 80-day pilot-scale composting. Compared with the Fenton pretreatment, the contents of Fe (II) and hydroxyl radicals (·OH) in the SW4 treatment increased by 20.25 %-54.55 % and 6.39 %-71.00 %, respectively. This confirmed the role of OA in protecting Fe (II) and maintaining the generation of ·OH during the composting. Compared with Control, Fenton-like reagent amendment facilitated decomposition of dissolved organic carbon and total organic matter by 20.53 % and 25.37 %, respectively, which led to a higher content of humic substances (141.81 mg/g) and a higher degree of polymerization (3.51) in SW4. Among all, the dissolved organic carbon in the compost substrate of SW4 treatment showed the highest level of aromatization and more refractory organic matter decomposition. The compact microbial co-occurrence network analysis exhibited the high-metabolic activity in Fenton-like treatment (SW4). Therefore, the probable mechanism of humification facilitation by Fenton-like reagent amendment in co-composting could be controlled by several processes: 1) generation of ·OH for facilitating the decomposition of organic matter, 2) disintegration of refractory lignocellulose substances by promoting the lignin pathway of humification, and 3) increasing the quantity and activity of microbes (i.e., Proteobacteria, Actinobacteriota, Chloroflexi, Ascomycota and Basidiomycota) involved in humification. This study provided a profound understanding of Fenton-like reagent amendments in co-composting of agricultural solid wastes and proposes a solution for enhancing the humification degree of compost products for agricultural use.

Key role of NH4+-N in the removal of oxacillin during managed aquifer recharge: Reconsidering the recharge limitation

Frequent occurrence of trace antibiotics in reclaimed water is concerning, which inevitably causes aquifer contamination in the case of managed aquifer recharge (MAR). Global governments have formulated strict reclaimed water standards to ensure the safety of water reuse. Recent studies have found that improved antibiotics removal is intimately associated with high ammonia-oxidizing activity. However, the role of NH4+-N in the removal of residual antibiotics of reclaimed water during MAR remains unknown. NH4+-N removal and the effects of ammonia oxidation on antibiotics biodegradation in the aquifer are the most significant facts for solving the above collision. In this work, the effects of NH4+-N (0, 1 and 5 mg/L) in a model refractory antibiotic (oxacillin (OXA), 100 μg/L) attenuation were deciphered by employing three individual simulated MAR columns, which so called N0, N1 and N5. The results showed that 5 mg/L NH4+-N in influent upregulated the abundance of amo genes by 28.9 %-68.0 % in N5. And the enriched functional genes encoding key degradation enzymes enhanced the OXA removal by 18.7 % and alleviated the oxidative stress caused by antibiotics. Subsequently, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) and human bacterial pathogens (HBPs) abundance were all significantly decreased. Moreover, the intimate association between ammonia-oxidizing microorganisms (AOM) and candidate OXA degraders based on microbial network analysis further supported the significance of AOM on OXA biodegradation. This study provides comprehensive evidence that appropriate amounts of NH4+-N are beneficial in antibiotics and antibiotic resistance risk reduction, providing compelling insights for refine NH4+-N recharge limitation.

Synergy between Nitrogen Removal and Fermentation Bacteria Ensured Efficient Nitrogen Removal of a Mainstream Anammox System at Low Temperatures.

Simultaneous partial nitrification, anammox, denitrification, and fermentation (SNADF) is a novel process achieving simultaneous advanced sludge reduction and nitrogen removal. The influence of low temperatures on the SNADF reactor was explored to facilitate the application of mainstream anammox. When temperature decreased from 32 to 16 °C, efficient nitrogen removal was achieved, with a nitrogen removal efficiency of 81.9-94.9%. Microbial community structure analysis indicated that the abundance of Candidatus Brocadia (dominant anaerobic ammonia oxidizing bacteria (AnAOB) in the system) increased from 0.03% to 0.18%. The abundances of Nitrospira and Nitrosomonas increased from 1.6% and 0.16% to 2.5% and 1.63%, respectively, resulting in an increase in the ammonia-oxidizing bacteria (AOB) to nitrite-oxidizing bacteria (NOB) abundance ratio from 0.1 to 0.64. This ensured sufficient nitrite for AnAOB, promoting nitrogen removal. In addition, Candidatus Competibacter, which plays a role in partial denitrification, was the dominant denitrification bacteria (DNB) and provided more nitrite for AnAOB, facilitating AnAOB enrichment. Based on the findings from microbial correlation network analysis, Nitrosomonas (AOB), Thauera, and Haliangium (DNB), and A4b and Saprospiraceae (fermentation bacteria), were center nodes in the networks and therefore essential for the stability of the SNADF system. Moreover, fermentation bacteria, DNB, and AOB had close connections in substrate cooperation and resistance to adverse environments; therefore, they also played important roles in maintaining stable nitrogen removal at low temperatures. This study provided new suggestions for mainstream anammox application.

Modulations in gastrointestinal microbiota during postpartum period fulfill energy requirements and maintain health of lactating Tibetan cattle.

Postpartum period of dairy cattle is an important phase of their life mainly associated with the changes in physiology, rumen function, and energy metabolism. Studies have shown that gut microbial composition undergoes drastic changes during the postpartum period. However, little is known about the temporal variations in digestive tract microbiota in postpartum Tibetan cattle. The aim of this study was to investigate the temporal variations in blood metabolites, ruminal fermentation, and microbial community of oral, rumen, and gut in lactating Tibetan cattle during postpartum. We collected blood, saliva, rumen fluid, and fecal samples from lactating Tibetan cattle during 1st week (1 W), the 2nd week (2 W), the 1st month (1 M), and the 2nd month (2 M) of the postpartum period. The microbiota of saliva, rumen fluid, and fecal samples were assessed using 16S rRNA sequencing. The rumen volatile fatty acid and blood parameters were also quantified. The content of volatile fatty acids (VFAs) and blood parameters showed opposite tendency to each other and reached to stability at 2 M. Rumen microbiota showed the highest alpha diversity compared to other two sites. At phylum level, the oral cavity was dominated by Proteobacteria, while most dominant phylum in rumen and feces were Firmicutes and Bacteroidetes, respectively. The dominant genera in oral cavity were Moraxella and Bibersteinia, while genera Prevotella 1 and Ruminococcaceae UCG-005 were dominant in rumen and fecal samples, respectively. Microbial network analysis revealed that most of the active genera in all networks belonged to phylum Firmicutes, indicating the importance of this phyla during postpartum period of lactating cattle. The functional analysis revealed distinct division of labor among three gastrointestinal sites associated with defense, fatty acid synthesis, and maintaining health of host. All in all, our findings provide insights into the metabolic and microbial changes of lactating Tibetan cattle and help to the improvement of the management strategies.

Gut microbiome reveals contrasting enterotypes and health statuses of semi-wild Saiga antelopes (Saiga tatarica)

Gut microbiome studies based on fecal samples can non-invasively reflect the survival and health status of endangered species. This study presents the first characterization of the gut microbiome in the semi-wild population of the critically endangered Saiga antelope (Saiga tatarica), unveiling the existence of two distinct enterotypes within the semi-wild Saiga: the Oscillospiraceae UCG-005 enterotype and the Arthrobacter enterotype. These enterotypes show significant differences in microbiome diversity, composition, and predicted functions. The Arthrobacter enterotype has lower alpha diversity, fewer short-chain fatty acids (SCFAs)-producing bacteria, more potential pathogens, lower energy metabolism and higher lipid metabolism abundance. The findings imply that Saiga with the Arthrobacter enterotype have lower energy utilization efficiency and higher disease risks, particularly for obesity. Microbial correlation network analysis indicates SCFAs-producing bacteria play a key role in the formation of these enterotypes. This suggests that next-generation probiotics, primarily composed of SCFAs-producing bacteria, could be used to regulate and improve the health of the Saiga. Additionally, the similarity of the enterotype associated with a healthier survival state to that of wild counterparts suggests that incorporating gut microbiome monitoring into the key indicators for the reintroduction of endangered species could be significant for wildlife conservation and management.

Rumen microbiota helps Tibetan sheep obtain energy more efficiently to survive in the extreme environment of the Qinghai-Tibet Plateau.

T-sheep and H-sheep exhibit different environmental adaptability and production performance. The rumen microbiome has co-evolved with hosts and plays a vital role in nutrient digestion and energy metabolism. In our previous study, we found that T-sheep have a higher efficiency in energy metabolism than H-sheep, but the rumen microbial community remains unclear. In this study, we determined the rumen bacterial profile and rumen fermentation parameters to reveal the bacterial profiles and predictive functions among breeds and diets with four different energy levels, as well as the correlation between bacterial profiles and rumen fermentation characteristics. The results showed that the rumen total volatile fatty acids (VFAs), acetate, butyrate, total branched-chain VFAs, iso-butyrate, and iso-valerate were higher in T-sheep than H-sheep. The alpha diversity of ruminal bacteria is not affected by dietary energy, but it shows a distinction between the sheep breeds. Specifically, T-sheep rumen bacteria exhibit higher alpha diversity than H-sheep. The beta diversity of ruminal bacteria is not influenced by dietary energy or sheep breeds, indicating similar communities of ruminal bacteria between different diets and sheep breeds. The phyla of Bacteroidetes and Firmicutes predominate in the rumen, with a higher relative abundance of Firmicutes observed in T-sheep than H-sheep. The two most abundant genera in the rumen were Prevotella 1 and Rikenellaceae RC9 gut group. Prevotella 1 is the predominant bacterial genus in the rumen of H-sheep, while the Rikenellaceae RC9 gut group dominates in the rumen of T-sheep. Microbial co-occurrence network analysis reveals that variations in rumen fermentation characteristics result from differences in module abundance, with a higher abundance of VFA-producing modules observed in the rumen of T-sheep. Microbial function prediction analysis showed that dietary energy rarely alters the functional composition of rumen bacteria. However, there were differences in the functions of rumen bacteria between sheep breeds, with T-sheep showing a greater emphasis on energy metabolism-related functions, while H-sheep showed a greater emphasis on protein metabolism-related functions. These findings provide evidence of the special rumen microbial community that helps T-sheep efficiently obtain energy from low-protein and low-energy diets, enabling them to survive in the extreme environment of the Qinghai-Tibet Plateau.

Response of soil fungi to textile dye contamination

This study examines the impact of textile dye contamination on the structure of soil fungal communities near a Shaoxing textile dye factory. We quantified the concentrations of various textile dyes, including anthraquinone azodye and phthalocyanine, which ranged from 20.20 to 140.62 mg kg^-1, 102.01–698.12 mg kg^-1, and 7.78–42.65 mg kg^-1, respectively, within a 1000 m radius of the factory. Our findings indicate that as dye concentration increases, the biodiversity of soil fungi, as measured by the Chao1 index, decreases significantly, highlighting the profound influence of dye contamination on fungal community structure. Additionally, microbial correlation network analysis revealed a reduction in fungal interactions correlating with increased dye concentrations. We also observed that textile dyes suppressed carbon and nitrogen metabolism in fungi while elevating the transcription levels of antioxidant-related genes. Enzymes such as lignin peroxidase (LiP), manganese peroxidase (MnP), laccase (Lac), dye-decolorizing peroxidases (DyPs), and versatile peroxidase (VP) were upregulated in contaminated soils, underscoring the critical role of fungi in dye degradation. These insights contribute to the foundational knowledge required for developing in situ bioremediation technologies for contaminated farmlands.

Reveling the micromolecular biological mechanism of acetate, thiosulfate and Fe0 in ecological floating beds for treating low C/N wastewater: Insight into nitrogen removals and greenhouse gases reductions

Selecting an appropriate electron donor to enhance nitrogen removal for treating low C/N wastewater in ecological floating beds (EFBs) is controversy. In this study, a systematic and comprehensive evaluation of sodium acetate (EFB-C), sodium thiosulfate (EFB-S) and iron scraps (EFB-Fe) was performed in a 2-year experiment on long-term viability including nitrogen removal and greenhouse gas emissions associated with key molecular biological mechanisms. The results showed that EFB-C (43–85 %) and EFB-S (40–88 %) exhibited superior total nitrogen (TN) removal. Temperature and hydraulic retention time (HRT) have significant impacts on TN removal of EFB-Fe, however, it could reach 86 % under high temperature (30–35 °C) and a long HRT (3 days), and it has lowest N2O (0–6.2 mg m−2 d−1) and CH4 (0–5.3 mg m−2 d−1) fluxes. Microbial network analysis revealed that the microbes changed from competing to cooperating after adding electron donors. A higher abundance of anammox genera was enriched in EFB-Fe. The Mantel's test and structural equation model provided proof of the differences, which showed that acetate and thiosulfate were similar, whereas Fe0 was different in the nitrogen removal mechanism. Molecular biology analyses further verified that heterotrophic, autotrophic, and mixotrophic coupled with anammox were the main TN removal pathways for EFB-C, EFB-S, and EFB-Fe, respectively. These findings provide a better understanding of the biological mechanisms for selecting appropriate electron donors for treating low C/N wastewater.

Host-associated helminth diversity and microbiome composition contribute to anti-pathogen defences in tropical frogs impacted by forest fragmentation.

Habitat fragmentation can negatively impact wildlife populations by simplification of ecological interactions, but little is known about how these impacts extend to host-associated symbiotic communities. The symbiotic communities of amphibians play important roles in anti-pathogen defences, particularly against the amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd). In this study, we analyse the role of macroparasitic helminth communities in concert with microbial communities in defending the host against Bd infection within the context of forest fragmentation. We found that skin microbial and helminth communities are disrupted at fragmented habitats, while gut microbiomes appear more resilient to environmental change. We also detected potential protective roles of helminth diversity and anti-pathogen microbial function in limiting Bd infection. Microbial network analysis revealed strong patterns of structure in both skin and gut communities, with helminths playing central roles in these networks. We reveal consistent roles of microbial and helminth diversity in driving host-pathogen interactions and the potential implications of fragmentation on host fitness.

Tea and Pleurotus ostreatus intercropping modulates structure of soil and root microbial communities.

Intercropping with Pleurotus ostreatus has been demonstrated to increase the tea yield and alleviate soil acidification in tea gardens. However, the underlying mechanisms remain elusive. Here, high-throughput sequencing and Biolog Eco analysis were performed to identify changes in the community structure and abundance of soil microorganisms in the P. ostreatus intercropped tea garden at different seasons (April and September). The results showed that the soil microbial diversity of rhizosphere decreased in April, while rhizosphere and non-rhizosphere soil microbial diversity increased in September in the P. ostreatus intercropped tea garden. The diversity of tea tree root microorganisms increased in both periods. In addition, the number of fungi associated with organic matter decomposition and nutrient cycling, such as Penicillium, Trichoderma, and Trechispora, was significantly higher in the intercropped group than in the control group. Intercropping with P. ostreatus increased the levels of total nitrogen (TN), total phosphorus (TP), and available phosphorus (AP) in the soil. It also improved the content of secondary metabolites, such as tea catechins, and polysaccharides in tea buds. Microbial network analysis showed that Unclassified_o__Helotiales, and Devosia were positively correlated with soil TN and pH, while Lactobacillus, Acidothermus, and Monascus were positively correlated with flavone, AE, and catechins in tea trees. In conclusion, intercropping with P. ostreatus can improve the physical and chemical properties of soil and the composition and structure of microbial communities in tea gardens, which has significant potential for application in monoculture tea gardens with acidic soils.